6EBV | pdb_00006ebv

Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Deoxy-N7-Pan

PDB DOI: https://doi.org/10.2210/pdb6EBV/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-08-07 Released: 2019-08-07
Deposition Author(s): Chen, Y., Antoshchenko, T., Strauss, E., Barnard, L., Huang, Y.H., Park, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.280 (Depositor), 0.271 (DCC)
R-Value Work:
0.228 (Depositor)
R-Value Observed:
0.231 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-based identification of uncompetitive inhibitors for Staphylococcus aureus pantothenate kinase.

Chen, Y., Antoshchenko, T., Strauss, E., Barnard, L., Huang, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 119.8 kDa
Atom Count: 8,349
Modeled Residue Count: 1,064
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II pantothenate kinase	A, B, C, D	267	Staphylococcus aureus	Mutation(s): 0 Gene Names: coaW, BTN44_13005, C3B39_13135, EP54_10775, EQ90_06670, HMPREF3211_02599 EC: 2.7.1.33
UniProt
Find proteins for Q2FWC7 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FWC7 Go to UniProtKB: Q2FWC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FWC7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
27Q Query on 27Q Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	N-heptyl-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide C₁₆ H₃₃ N₂ O₇ P QTSWMJJVYAHWSJ-AWEZNQCLSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.280 (Depositor), 0.271 (DCC)
R-Value Work: 0.228 (Depositor)
R-Value Observed: 0.231 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.8	α = 90
b = 56.72	β = 99.81
c = 133.62	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
BUSTER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-08-07

Deposition Author(s):

Antoshchenko, T.

Revision History (Full details and data files)

Version 1.0: 2019-08-07
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.